20.20(S11):Advanced topics
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20.385: Advanced Topics in Synthetic Biology
Assignments
Homework dropbox is here
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Part 1: Readings
Instructions for these assignment are here |
Part 2: Team Mentoring
Instructions for these assignments are here |
Reading Schedule
Discussions will be 1 hour long during Wednesday 2-5 studio block
26-152
| TOPIC | DATE | Discussion leader(s) | Discussion paper(s) | Related paper(s) to enjoy |
| Preview of 20.385 | Wed Feb 2 | Natalie Kuldell | preview of 20.385 | before next week read
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| Parts™ | Wed Feb 9 | Natalie Kuldell ppt is here |
Turning lambda Cro into a transcriptional activatorBushman FD, Ptashne M.Cell. (1988) Jul 15;54(2):191-7. PMID: 2968842 |
Improving the Lac System for Synthetic Biology Penumetcha, P., et al. Bios (2011) 81(1):7-15. |
| Transcription-based Logic Devices |
Wed Feb 16 | Pei-Ann, Jessica ppt is here |
Environmental signal integration by a modular AND gate Anderson JC, Voigt C, Arkin, AP Molecular systems biology (2007) 3:133 PMID: 17700541 |
A synthetic oscillatory network of transcriptional regulators Elowitz, MB, and Leibler, S. Nature (2000) 403, 335–338 |
| Protein Design: directed evolution |
Wed Feb 23 | Yuan, Amber ppt is here |
De Novo Designed Proteins from a Library of Artificial Sequences Function in Esherichia Coli and Enable Cell Growth Fisher MA, et al. PLoS One (2011)6(1):e15364 DOI: 10.1371/journal.pone.0015364 |
Directed evolution of recombinase specificity by split gene reassembly Gersbach, CA, et al. NAR (2010) 38(12): 4198-4206-1543 DOI: 10.1093/nar/gkq125 |
| RNA Engineering |
Wed Mar 2 | Andrew, Tina ppt is here |
Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins Culler, SJ, Hoff, KG, Smolke, CD. Science (2010) 330:1251-1255 DOI: 10.1126/science.1192128 |
The Case for RNA Chang, CL, Arkin AP. Science (2010) 330:1185-1186 DOI: 10.1126/science.1199495 |
| Tuning the system: Network Composition |
Wed Mar 10 before 3 ideas presentations, meet in 4-163 |
Colin, Raven ppt is here |
A modular positive feedback-based gene amplifier Nistala GJ et al. JBE (2010) 4:4 DOI: 10.1186/1754-1611-4-4 |
A fast, robust and tunable synthetic gene oscillator Stricker, J. et al. Nature (2008) 456, 516–519 PMID: 18971928 |
| (re)Programming Systems |
Wed Mar 16 | Patrick, Nick ppt is here |
Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA Warren L, et al. Cell Stem Cell (2010) 7:618-630 DOI:10.1016/j.stem.2010.08.012 |
Reprogramming bacteria to seek and destroy an herbicide Sinha, J. et al. Nature Chemical Biology (2010)6: 464–470 doi:10.1038/nchembio.369 |
| Spring Break Mar 21-25 | No class all week | |||
|---|---|---|---|---|
| DNA construction and editing technologies |
Wed Mar 30 | Raven, Andrew Andrew's ppt is here Raven's ppt is here |
Programming cells by multiplex genome engineering and accelerated evolution Wang HH, et al. Nature (2009) Aug 13;460(7257):894-8. PMID: 19633652 |
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides Stemmer WP, et al. Gene (1995) 164(1):49-53 PMID: 7590320 |
| Measurement technologies |
Wed Apr 6 before tech spec review, meet in 56-114 |
Nick ppt is here |
Nascent transcript sequencing visualizes transcription at nucleotide resolutionChurchman LS and Weissman JS.Nature (2011)469:368-373 DOI: 10.1038/nature09652 | Measuring the activity of BioBrick promoters using an in vivo reference standard Kelly J, et al. Journal of Biological Engineering (2009) 3:4 doi:10.1186/1754-1611-3-4 |
| Chassis |
Wed Apr 13 | Jessica, Tina Tina's ppt is here Jessica will present next week |
Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system Shin J, and Noireaux, V. JBE (2010) 4:9 DOI: 10.1186/1754-1611-4-9 |
Emergent properties of reduced-genome Escherichia coli. Pósfai G, et al. Science.(2006)312(5776):1044-6. PMID: 16645050 |
| Signal Connectivity |
Wed Apr 20 | Amber (will present Skerker paper next week) Jessica's ppt is here |
Rewiring the specificity of two-component signal transduction systems Skerker JM, et al. Cell (2008)133(6):1043-54. PMID: 18555780 |
Tunable Signal Processing in Synthetic MAP Kinase Cascades O'Shaughnessy, EC, et al. Cell(2011) 144:119-131 DOI: 10.1016/j.cell.2010.12.014 |
| Metabolic Engineering | Wed Apr 27 | Yuan Amber's ppt is here Yuan's ppt is here |
Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli.Moon TS et al. Metabolic Engineering (2010) 12: 298-305 (2010) PMID: 20117231 | Production of the antimalarial drug precursor artemisinic acid in engineered yeast Ro DK, et al. Nature (2006) 440, 940–943 PMID: 16612385 |
| Cell Cell Communication/System Ecology | Wed May 4 | Colin ppt is here |
Robust multicellular computing using genetically encoded NOT gates and chemical 'wires' Tamsir, a., Tabor, J.J., Voigt, C.A. Nature 2011 Jan 13;469:212-215. DOI: 10.1038/nature09565 + supplementary info |
Division of logic labour Li B and You L.Nature (2011) 469:171-172 DOI:10.1038/469171a |
| Property rights in synthetic biology | Wed May 11 before final presentations, meet in 56-114 |
Pei ppt is here |
Synthetic biology: caught between property rights, the public domain, and the commons Rai A, Boyle J. PLoS Biol. (2007)5(3):e58 PMID: 17355173 |
Patents and Translational Research in Genomics Kaye J, Hawkins N, and Taylor J. Nature Biotech (2007) 25(7): 739–741.doi: 10.1038/nbt0707-739. |
| Safety! | Wed May 11 before final presentations, meet in 56-114 |
Patrick ppt is here |
Managing the unimaginable. Regulatory responses to the challenges posed by synthetic biology and synthetic genomics. Samuel GN, Selgelid MJ, Kerridge I. EMBO reports (2009) 10(1):7-11. DOI: 10.1038/embor.2008.232 |
Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses? Michael Specter New Yorker article |
